1-31790901-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144569.7(SPOCD1):c.3353G>A(p.Arg1118His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000417 in 1,582,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1118C) has been classified as Likely benign.
Frequency
Consequence
NM_144569.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000463 AC: 10AN: 215780Hom.: 0 AF XY: 0.0000427 AC XY: 5AN XY: 117014
GnomAD4 exome AF: 0.0000447 AC: 64AN: 1430744Hom.: 0 Cov.: 31 AF XY: 0.0000324 AC XY: 23AN XY: 709132
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3353G>A (p.R1118H) alteration is located in exon 16 (coding exon 15) of the SPOCD1 gene. This alteration results from a G to A substitution at nucleotide position 3353, causing the arginine (R) at amino acid position 1118 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at